* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/CohortSurvival.Rcheck’
* using R Under development (unstable) (2024-05-02 r86510)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 18.1.5
    flang-new version 18.1.5
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘CohortSurvival/DESCRIPTION’ ... OK
* this is package ‘CohortSurvival’ version ‘0.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CohortSurvival’ can be installed ... [12s/48s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/CohortSurvival-00install.html' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [20s/87s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [69s/68s] ERROR
  Running ‘testthat.R’ [69s/66s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(CohortSurvival)
  > 
  > test_check("CohortSurvival")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 45 | PASS 1 ]
  
  ══ Skipped tests (45) ══════════════════════════════════════════════════════════
  • On CRAN (45): 'test-benchmarkCohortSurvival.R:2:3',
    'test-benchmarkCohortSurvival.R:63:3', 'test-addCohortSurvival.R:71:3',
    'test-addCohortSurvival.R:158:3', 'test-addCohortSurvival.R:271:3',
    'test-addCohortSurvival.R:377:3', 'test-addCohortSurvival.R:489:3',
    'test-addCohortSurvival.R:567:3', 'test-addCohortSurvival.R:667:3',
    'test-addCohortSurvival.R:753:3', 'test-generateDeathCohort.R:2:3',
    'test-generateDeathCohort.R:62:3', 'test-generateDeathCohort.R:129:3',
    'test-generateDeathCohort.R:195:3', 'test-generateDeathCohort.R:262:3',
    'test-generateDeathCohort.R:351:3', 'test-generateDeathCohort.R:451:3',
    'test-mockMGUS2cdm.R:2:3', 'test-plotSurvival.R:2:3',
    'test-plotSurvival.R:19:3', 'test-plotSurvival.R:37:3',
    'test-plotSurvival.R:57:3', 'test-plotSurvival.R:77:3',
    'test-plotSurvival.R:98:3', 'test-plotSurvival.R:129:3',
    'test-plotSurvival.R:149:3', 'test-tableSurvival.R:2:3',
    'test-tableSurvival.R:51:3', 'test-estimateSurvival.R:88:3',
    'test-estimateSurvival.R:127:3', 'test-estimateSurvival.R:177:3',
    'test-estimateSurvival.R:344:3', 'test-estimateSurvival.R:557:3',
    'test-estimateSurvival.R:708:3', 'test-estimateSurvival.R:1225:3',
    'test-estimateSurvival.R:1351:3', 'test-estimateSurvival.R:1373:3',
    'test-estimateSurvival.R:1408:3', 'test-estimateSurvival.R:1484:3',
    'test-estimateSurvival.R:1676:3', 'test-estimateSurvival.R:1800:3',
    'test-estimateSurvival.R:1830:3', 'test-estimateSurvival.R:1849:3',
    'test-estimateSurvival.R:1883:3', 'test-estimateSurvival.R:2014:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-estimateSurvival.R:9:3'): mgus example: no Competing risk ──────
  Error in `validateSummariseResult(x)`: ids are not unique in settings
  Backtrace:
       ▆
    1. ├─... %>% asSurvivalResult() at test-estimateSurvival.R:9:3
    2. ├─CohortSurvival::asSurvivalResult(.)
    3. │ └─omopgenerics::newSummarisedResult(result)
    4. │   └─omopgenerics:::assertClass(x = x, class = "data.frame")
    5. │     ├─base::paste0(...)
    6. │     └─base::paste0(base::class(x), collapse = ", ")
    7. └─CohortSurvival::estimateSingleEventSurvival(...)
    8.   └─omopgenerics::newSummarisedResult(surv_estimates)
    9.     └─omopgenerics:::validateSummariseResult(x)
   10.       └─cli::cli_abort("ids are not unique in settings")
   11.         └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 45 | PASS 1 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [89s/281s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘a01_Single_event_of_interest.Rmd’ using rmarkdown

Quitting from lines  at lines 47-54 [unnamed-chunk-5] (a01_Single_event_of_interest.Rmd)
Error: processing vignette 'a01_Single_event_of_interest.Rmd' failed with diagnostics:
ids are not unique in settings
--- failed re-building ‘a01_Single_event_of_interest.Rmd’

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a02_Competing_risk_survival.Rmd’ using rmarkdown

Quitting from lines  at lines 55-64 [unnamed-chunk-5] (a02_Competing_risk_survival.Rmd)
Error: processing vignette 'a02_Competing_risk_survival.Rmd' failed with diagnostics:
Can't rename columns that don't exist.
✖ Column `V2` doesn't exist.
--- failed re-building ‘a02_Competing_risk_survival.Rmd’

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following files failed:
  ‘a01_Single_event_of_interest.Rmd’ ‘a02_Competing_risk_survival.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [8s/47s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs